Immunoglobulin and T cell receptor genes: IMGT® and the birth and rise of immunoinformatics

Frontiers in Immunology

Volumn 5, Issue FEB, 2014, Pages

  Lefranc, Marie Paule ^a  

^a CNRS and University Montpellier II   (France)

Author keywords

IMGT; IMGT Collier de Perles; IMGT ONTOLOGY; Immunogenetics; Immunoglobulin; Immunoinformatics; Major histocompatibility; T cell receptor

Indexed keywords

ALEMTUZUMAB; EPITOPE; IMMUNOGLOBULIN E; IMMUNOGLOBULIN LAMBDA CHAIN; IMMUNOGLOBULIN M; MAJOR HISTOCOMPATIBILITY ANTIGEN; T LYMPHOCYTE RECEPTOR ALPHA CHAIN;

ANTIBODY COMBINING SITE; ARTICLE; BIOINFORMATICS; CYTOTOXICITY; DNA POLYMORPHISM; GENETIC DATABASE; GENETIC ENGINEERING; HIGH THROUGHPUT SEQUENCING; HOMEOSTASIS; HUMAN; IMGT TOOL; IMMUNE RESPONSE; IMMUNOGENICITY; IMMUNOGLOBULIN GENE; IMMUNOINFORMATICS; NONHUMAN; NUCLEOTIDE SEQUENCE; T LYMPHOCYTE RECEPTOR GENE; THREE DIMENSIONAL IMAGING;

EID: 84895541683     PISSN: None     EISSN: 16643224     Source Type: Journal    
DOI: 10.3389/fimmu.2014.00022     Document Type: Article

References (106)

1. Lefranc M-P, Giudicelli V, Ginestoux C, Jabado-Michaloud J, Folch G, Bellahcene F, et al. IMGT®, the international ImMunoGeneTics information system®. Nucleic Acids Res (2009) 37:D1006-12. doi:10.1093/nar/gkn838.
2. Lefranc M-P, Lefranc G. The Immunoglobulin FactsBook. London: Academic Press (2001).
3. Lefranc M-P, Lefranc G. The T Cell Receptor FactsBook. London: Academic Press (2001).
4. Lefranc M-P. Nomenclature of the human immunoglobulin genes. In: Coligan JE, Bierer BE, Margulies DE, Shevach EM, Strober W, editors. Current Protocols in Immunology. Hoboken NJ: John Wiley and Sons (2000). p. A.11-137.
5. Lefranc M-P. Nomenclature of the human T cell receptor genes. In: Coligan JE, Bierer BE, Margulies DE, Shevach EM, Strober W, editors. Current Protocols in Immunology. Hoboken NJ: John Wiley and Sons (2000). p. A.10.1-A.10.23.
6. Smith KA. Toward a molecular understanding of adaptive immunity: a chronology, part I. Front Immunol (2012) 3:369. doi:10.3389/fimmu.2012.00369.
7. Smith KA. Toward a molecular understanding of adaptive immunity: a chronology, part II. Front Immunol (2012) 3:364. doi:10.3389/fimmu.2012.00364.
8. Lefranc M-P, Duprat E, Kaas Q, Tranne M, Thiriot A, Lefranc G. IMGT unique numbering for MHC groove G-DOMAIN and MHC superfamily (MhcSF) G-LIKE-DOMAIN. Dev Comp Immunol (2005) 29:917-38. doi:10.1016/j.dci.2005.03.003.
9. Giudicelli V, Duroux P, Ginestoux C, Folch G, Jabado-Michaloud J, Chaume D, et al. IMGT/LIGM-DB, the IMGT® comprehensive database of immunoglobulin and T cell receptor nucleotide sequences. Nucleic Acids Res (2006) 34:D781-4. doi:10.1093/nar/gkj088.
10. Giudicelli V, Chaume D, Lefranc M-P. IMGT/GENE-DB: a comprehensive database for human and mouse immunoglobulin and T cell receptor genes. Nucleic Acids Res (2005) 33:D256-61. doi:10.1093/nar/gki010.
11. Kaas Q, Ruiz M, Lefranc M-P. IMGT/3Dstructure-DB and IMGT/ StructuralQuery, a database and a tool for immunoglobulin, T cell receptor and MHC structural data. Nucleic Acids Res (2004) 32:D208-10. doi:10.1093/nar/gkh042.
12. Ehrenmann F, Kaas Q, Lefranc M-P. IMGT/3Dstructure-DB and IMGT/DomainGapAlign: a database and a tool for immunoglobulins or antibodies, T cell receptors, MHC, IgSF and MhcSF. Nucleic Acids Res (2010) 38:D301-7. doi:10.1093/nar/gkp946.
13. Ehrenmann F, Lefranc M-P. IMGT/3Dstructure-DB: querying the IMGT database for 3D structures in immunology and immunoinformatics (IG or antibodies, TR, MH, RPI, and FPIA). Cold Spring Harb Protoc (2011) 6:750-61. doi:10.1101/pdb.prot5637.
14. Poiron C, Wu Y, Ginestoux C, Ehrenmann F, Duroux P, Lefranc M-P. IMGT/mAb-DB: The IMGT® Database for Therapeutic Monoclonal Antibodies, 11èmes Journées Ouvertes de Biologie, Informatique et Mathématiques (JOBIM). Montpellier (2010). Poster 13, Available from: http://www.jobim2010.fr/indexe662.html?q=en/node/56.
15. Giudicelli V, Chaume D, Lefranc M-P. IMGT/V-QUEST, an integrated software for immunoglobulin and T cell receptor V-J and V-D-J rearrangement analysis. Nucleic Acids Res (2004) 32:W435-40. doi:10.1093/nar/gkh412.
16. Giudicelli V, Lefranc M-P. Interactive IMGT on-line tools for the analysis of immunoglobulin and T cell receptor repertoires. In: Veskler BA, editor. New Research on Immunology. New York: Nova Science Publishers Inc (2005). p. 77-105.
17. Brochet X, Lefranc M-P, Giudicelli V. IMGT/V-QUEST: the highly customized and integrated system for IG and TR standardized V-J and V-D-J sequence analysis. Nucleic Acids Res (2008) 36:W503-8. doi:10.1093/nar/gkn316.
18. Giudicelli V, Lefranc M-P. IMGT® standardized analysis of immunoglobulin rearranged sequences. In: Ghia P, Rosenquist R, Davi F, editors. Immunoglobulin Gene Analysis in Chronic Lymphocytic Leukemia. Italy: Wolters Kluwer Health (2008). p. 33-52.
19. Giudicelli V, Brochet X, Lefranc M-P. IMGT/V-QUEST: IMGT standardized analysis of the immunoglobulin (IG) and T cell receptor (TR) nucleotide sequences. Cold Spring Harb Protoc (2011) 6:695-715. doi:10.1101/pdb.prot5633.
20. Alamyar E, Duroux P, Lefranc M-P, Giudicelli V. IMGT® tools for the nucleotide analysis of immunoglobulin (IG) and T cell receptor (TR) V-(D)-J repertoires, polymorphisms, and IG mutations: IMGT/V-QUEST and IMGT/HighV-QUEST for NGS. In: Christiansen F, Tait B, editors. Methods Mol Biol. New York: Humana Press, Springer (2012) 882:569-604. doi:10.1007/978-1-61779-842-9_32.
21. Yousfi Monod M, Giudicelli V, Chaume D, Lefranc M-P. IMGT/ JunctionAnalysis: the first tool for the analysis of the immunoglobulin and T cell receptor complex V-J and V-D-J JUNCTIONs. Bioinformatics (2004) 20:i379-85. doi:10.1093/bioinformatics/bth945.
22. Giudicelli V, Lefranc M-P. IMGT/JunctionAnalysis: IMGT standardized analysis of the V-J and V-D-J junctions of the rearranged immunoglobulins (IG) and T cell receptors (TR). Cold Spring Harb Protoc (2011) 6:716-25. doi:10.1101/pdb.prot5634.
23. Giudicelli V, Protat C, Lefranc M-P. The IMGT strategy for the automatic annotation of IG and TR cDNA sequences: IMGT/Automat. In: Proceedings of the European Conference on Computational Biology (ECCB 2003)," Data and Knowledge Bases, Poster DKB_31, ECCB. Paris: Institut National de Recherche en Informatique et en Automatique (2003). pp. 103-104.
24. Giudicelli V, Chaume D, Jabado-Michaloud J, Lefranc M-P. Immunogenetics sequence annotation: the strategy of IMGT based on IMGT-ONTOLOGY. Stud Health Technol Inform (2005) 116:3-8.
25. Alamyar E, Giudicelli V, Shuo L, Duroux P, Lefranc M-P. IMGT/HighV-QUEST: the IMGT® web portal for immunoglobulin (IG) or antibody and T cell receptor (TR) analysis from NGS high throughput and deep sequencing. Immunome Res (2012) 8(1):26. doi:10.1007/978-1-61779-842-9_32.
26. Li S, Lefranc M-P, Miles JJ, Alamyar E, Giudicelli V, Duroux P, et al. IMGT/HighV-QUEST paradigm for T cell receptor IMGT clonotype diversity and next generation repertoire immunoprofiling. Nat Commun (2013) 4:2333. doi:10.1038/ncomms3333.
27. Ehrenmann F, Lefranc M-P. IMGT/DomainGapAlign: IMGT standardized analysis of amino acid sequences of variable, constant, and groove domains (IG, TR, MH, IgSF, MhSF). Cold Spring Harb Protoc (2011) 6:737-49. doi:10.1101/pdb.prot5636.
28. Ehrenmann F, Lefranc M-P. IMGT/DomainGapAlign: the IMGT® tool for the analysis of IG, TR, MHC, IgSF and MhcSF domain amino acid polymorphism. In: Christiansen F, Tait B, editors. Methods Mol Biol. New York: Humana Press, Springer (2012) 882:605-33. doi:10.1007/978-1-61779-842-9_33.
29. Ehrenmann F, Giudicelli V, Duroux P, Lefranc M-P. IMGT/Collier de Perles: IMGT standardized representation of domains (IG, TR, and IgSF variable and constant domains, MH and MhSF groove domains). Cold Spring Harb Protoc (2011) 6:726-36. doi:10.1101/pdb.prot5635.
30. Lane J, Duroux P, Lefranc M-P. From IMGT-ONTOLOGY to IMGT/LIGMotif: the IMGT® standardized approach for immunoglobulin and T cell receptor gene identification and description in large genomic sequences. BMC Bioinformatics (2010) 11:223. doi:10.1186/1471-2105-11-223.
31. Pommié C, Levadoux S, Sabatier R, Lefranc G, Lefranc M-P. IMGT standardized criteria for statistical analysis of immunoglobulin V-REGION amino acid properties. J Mol Recognit (2004) 17:17-32. doi:10.1002/jmr.647.
32. Lefranc M-P. IMGT, the international ImMunoGeneTics information system. In: Bock G, Goode J editors. "Immunoinformatics: Bioinformatic Strategies for Better Understanding of Immune Function" Novartis Foundation Symposium, Vol. 254. Chichester: John Wiley and Sons (2003). pp. 126-126; discussion 136-142, 216-222, 250-252.
33. Lefranc M-P, Giudicelli V, Ginestoux C, Chaume D. IMGT, the international ImMunoGeneTics information system: the reference in immunoinformatics. Stud Health Technol Inform (2003) 95:74-9.
34. Lefranc M-P. IMGT databases, web resources and tools for immunoglobulin and T cell receptor sequence analysis. Leukemia (2003) 17(1):260-6. doi:10.1038/sj.leu.2402637.
35. Lefranc M-P. IMGT, the international ImMunoGenetics information system®. 2nd ed. In: Lo BKC, editor. Methods Mol Biol. Totowa, NJ: Humana Press (2004) 248:27-49.
36. Lefranc M-P. IMGT-ONTOLOGY and IMGT databases, tools and Web resources for immunogenetics and immunoinformatics. Mol Immunol (2004) 40(10):647-60. doi:10.1016/j.molimm.2003.09.006.
37. Lefranc M-P. IMGT, the international ImMunoGeneTics information system: a standardized approach for immunogenetics and immunoinformatics. Immunome Res (2005) 1:3. doi:10.1186/1745-7580-1-3.
38. Lefranc M-P. IMGT®, the international ImMunoGeneTics information system® for immunoinformatics. Methods for querying IMGT® databases, tools and Web resources in the context of immunoinformatics. In: Flower DR, editor. Methods Mol Biol. Totowa, NJ: Humana Press, Springer (2007) 409:19-42. doi:10.1007/978-1-60327-118-9_2.
39. Lefranc M-P. IMGT-ONTOLOGY, IMGT® databases, tools and Web resources for immunoinformatics. In: Schoenbach C, Ranganathan S, Brusic V editors. Immunoinformatics, Immunomics Reviews, Series of Springer Science and Business Media LLC, Vol. 1. New York: Springer (2008). pp. 1-18.
40. Lefranc M-P, Giudicelli V, Regnier L, Duroux P. IMGT®, a system and an ontology that bridge biological and computational spheres in bioinformatics. Brief Bioinform (2008) 9:263-75. doi:10.1093/bib/bbn014.
41. Lefranc M-P. IMGT®, the international ImMunoGeneTics information system® for immunoinformatics. Methods for querying IMGT® databases, tools and Web resources in the context of immunoinformatics. Mol Biotechnol (2008) 40:101-11. doi:10.1007/s12033-008-9062-7.
42. Lefranc M-P. Antibody databases and tools: the IMGT® experience. In: An Z, editor. Therapeutic Monoclonal Antibodies: From Bench to Clinic. Hoboken NJ: John Wiley and Sons (2009). p. 91-114.
43. Lefranc M-P. Antibody databases: IMGT®, a French platform of world-wide interest [in French]. Bases de données anticorps: IMGT®, une plate-forme française d'intérêt mondial. Med Sci (Paris) (2009) 25:1020-3. doi:10.1051/medsci/200925121020.
44. Ehrenmann F, Duroux P, Giudicelli V, Lefranc M-P. Standardized sequence and structure analysis of antibody using IMGT®. In: Kontermann R, Dübel S, editors. Antibody Engineering Vol. 2. Berlin: Springer-Verlag (2010). pp. 11-31.
45. Lefranc M-P. IMGT, the international ImMunoGeneTics information system. Cold Spring Harb Protoc (2011) 6:595-603. doi:10.1101/pdb.top115.
46. Lefranc M-P, Ehrenmann F, Ginestoux C, Duroux P, Giudicelli V. Use of IMGT® databases and tools for antibody engineering and humanization. Methods Mol Biol. New York: Humana Press, Springer (2012) 907:3-37.
47. Lefranc M-P. IMGT® information system. In: Dubitzky W, Wolkenhauer O, Cho K-H, Yokota H, editors. Encyclopedia of Systems Biology. New York: Springer Science+Business Media (2013). p. 959-64. doi:10.1007/978-1-4419-9863-7.
48. Lefranc M-P. WHO-IUIS Nomenclature Subcommittee for immunoglobulins and T cell receptors report. Immunogenetics (2007) 59:899-902. doi:10.1007/s00251-007-0260-4.
49. Lefranc M-P. WHO-IUIS Nomenclature Subcommittee for immunoglobulins and T cell receptors report August 2007, 13th International Congress of Immunology, Rio de Janeiro, Brazil. Dev Comp Immunol (2008) 32:461-3. doi:10.1016/j.dci.2007.09.008.
50. World Health Organization. International Nonproprietary Names (INN) for Biological and Biotechnological Substances (A Review). INN Working Document 05.179. (2012). Available from: http://www.who.int/medicines/services/inn/BioRev2012.pdf.
51. Lefranc M-P. Antibody nomenclature: from IMGT-ONTOLOGY to INN definition. MAbs (2011) 3(1):1-2. doi:10.4161/mabs.3.1.14151.
52. Giudicelli V, Lefranc M-P. Ontology for immunogenetics: IMGT-ONTOLOGY. Bioinformatics (1999) 15:1047-54. doi:10.1093/bioinformatics/15.12.1047.
53. Giudicelli V, Lefranc M-P. IMGT-ONTOLOGY 2012. Front Genet (2012) 3:79. eCollection 2012, doi:10.3389/fgene.2012.00079.
54. Giudicelli V, Lefranc M-P. IMGT-ONTOLOGY. In: Dubitzky W, Wolkenhauer O, Cho K-H, Yokota H, editors. Encyclopedia of Systems Biology. New York: Springer Science+Business Media (2013). p. 964-72. doi:10.1007/978-1-4419-9863-7.
55. Giudicelli V, Lefranc M-P. IMGT-ONTOLOGY: gestion et découverte de connaissances au sein d'IMGT. In: Hacid M-S, Kodratoff Y, Boulanger D editors. Extraction et gestion des connaissances (EGC'2003), Actes des troisièmes journées, Lyon, France, 22-24 janvier 2003. Revue des Sciences et Technologies de l'Information, RSTI, série Revue d'Intelligence Artificielle-Extraction des Connaissances et Apprentissage (RIA-ECA), Paris: Hermès Science Publications (2003). pp. 13-23.
56. Lefranc M-P, Giudicelli V, Ginestoux C, Bosc N, Folch G, Guiraudou D, et al. IMGT-ONTOLOGY for immunogenetics and immunoinformatics. In silico Biol (2004) 4:17-29.
57. Lefranc M-P, Clément O, Kaas Q, Duprat E, Chastellan P, Coelho I, et al. IMGT-choreography for immunogenetics and immunoinformatics. In silico Biol (2005) 5:45-60.
58. Duroux P, Kaas Q, Brochet X, Lane J, Ginestoux C, Lefranc M-P, et al. IMGT-Kaleidoscope, the formal IMGT-ONTOLOGY paradigm. Biochimie (2008) 90:570-83. doi:10.1016/j.biochi.2007.09.003.
59. Lefranc M-P. From IMGT-ONTOLOGY IDENTIFICATION Axiom to IMGT standardized keywords: for immunoglobulins (IG), T cell receptors (TR), and conventional genes. Cold Spring Harb Protoc (2011) 6:604-13. doi:10.1101/pdb.ip82.
60. Lefranc M-P. From IMGT-ONTOLOGY DESCRIPTION axiom to IMGT standardized labels: for immunoglobulin (IG) and T cell receptor (TR) sequences and structures. Cold Spring Harb Protoc (2011) 6:614-26. doi:10.1101/pdb.ip83.
61. Lefranc M-P. From IMGT-ONTOLOGY CLASSIFICATION axiom to IMGT standardized gene and allele nomenclature: for immunoglobulins (IG) and T cell receptors (TR). Cold Spring Harb Protoc (2011) 6:627-32. doi:10.1101/pdb.ip84.
62. Lefranc M-P. Unique database numbering system for immunogenetic analysis. Immunol Today (1997) 18:509. doi:10.1016/S0167-5699(97)01163-8.
63. Lefranc M-P. The IMGT unique numbering for immunoglobulins, T cell receptors and Ig-like domains. Immunologist (1999) 7:132-6. doi:10.1093/bfgp/elm032.
64. Lefranc M-P, Pommié C, Ruiz M, Giudicelli V, Foulquier E, Truong L, et al. IMGT unique numbering for immunoglobulin and T cell receptor variable domains and Ig superfamily V-like domains. Dev Comp Immunol (2003) 27:55-77. doi:10.1016/S0145-305X(02)00039-3.
65. Lefranc M-P, Pommié C, Kaas Q, Duprat E, Bosc N, Guiraudou D, et al. IMGT unique numbering for immunoglobulin and T cell receptor constant domains and Ig superfamily C-like domains. Dev Comp Immunol (2005) 29:185-203. doi:10.1016/j.dci.2004.07.003.
66. Lefranc M-P. IMGT unique numbering for the variable (V), constant (C), and groove (G) domains of IG, TR, MH, IgSF, and MhSF. Cold Spring Harb Protoc (2011) 6:633-42. doi:10.1101/pdb.ip85.
67. Ruiz M, Lefranc M-P. IMGT gene identification and Colliers de Perles of human immunoglobulins with known 3D structures. Immunogenetics (2002) 53:857-83. doi:10.1007/s00251-001-0408-6.
68. Kaas Q, Lefranc M-P. IMGT Colliers de Perles: standardized sequence-structure representations of the IgSF and MhcSF superfamily domains. Curr Bioinform (2007) 2:21-30. doi:10.1093/bfgp/elm032.
69. Kaas Q, Ehrenmann F, Lefranc M-P. IG, TR and IgSf, MHC and MhcSF: what do we learn from the IMGT Colliers de Perles? Brief Funct Genomic Proteomic (2007) 6:253-64. doi:10.1093/bfgp/elm032.
70. Lefranc M-P. IMGT Collier de Perles for the variable (V), constant (C), and groove (G) domains of IG, TR, MH, IgSF, and MhSF. Cold Spring Harb Protoc (2011) 6:643-51. doi:10.1101/pdb.ip86.
71. Robert R, Lefranc M-P, Ghochikyan A, Agadjanyan MG, Cribbs DH, Van Nostrand WE, et al. Restricted V gene usage and VH/VL pairing of mouse humoral response against the N-terminal immunodominant epitope of the amyloid β peptide. Mol Immunol (2010) 48(1-3):59-72. doi:10.1016/j.molimm.2010.09.012.
72. Ghia P, Stamatopoulos K, Belessi C, Moreno C, Stilgenbauer S, Stevenson FI, et al. ERIC recommendations on IGHV gene mutational status analysis in chronic lymphocytic leukemia. Leukemia (2007) 21:1-3. doi:10.1038/sj.leu.2404457.
73. Agathangelidis A, Darzentas N, Hadzidimitriou A, Brochet X, Murray F, Yan XJ, et al. Stereotyped B-cell receptors in one third of chronic lymphocytic leukemia: towards a molecular classification with implications for targeted therapeutic interventions. Blood (2012) 119(19):4467-75. doi:10.1182/blood-2011-11-393694.
74. Kostareli E, Gounari M, Janus A, Murray F, Brochet X, Giudicelli V, et al. Antigen receptor stereotypy across B-cell lymphoproliferations: the case of IGHV4-59/IGKV3-20 receptors with rheumatoid factor activity. Leukemia (2012) 26(5):1127-31. doi:10.1038/leu.2011.311.
75. Jefferis R, Lefranc M-P. Human immunoglobulin allotypes: possible implications for immunogenicity. MAbs (2009) 1(4):332-8. doi:10.4161/mabs.1.4.9122.
76. Lefranc M-P, Lefranc G. Human Gm, Km and Am allotypes and their molecular characterization: a remarkable demonstration of polymorphism. In: Christiansen F, Tait B, editors. Methods Mol Biol. New York: Humana Press, Springer (2012) 882:635-80. doi:10.1007/978-1-61779-842-9_34.
77. Dechavanne C, Guillonneau F, Chiappetta G, Sago L, Lévy P, Salnot V, et al. Mass spectrometry detection of G3m and IGHG3 alleles and follow-up of differential mother and neonate IgG3. PLoS One (2012) 7(9):e46097. doi:10.1371/journal.pone.0046097.
78. Magdelaine-Beuzelin C, Kaas Q, Wehbi V, Ohresser M, Jefferis R, Lefranc M-P, et al. Structure-function relationships of the variable domains of monoclonal antibodies approved for cancer treatment. Crit Rev Oncol Hematol (2007) 64:210-25. doi:10.1016/j.critrevonc.2007.04.011.
79. Pelat T, Bedouelle H, Rees AR, Crennell SJ, Lefranc M-P, Thullier P. Germline humanization of a non-human Primate antibody that neutralizes the anthrax toxin, by in vitro and in silico engineering. J Mol Biol (2008) 384:1400-7. doi:10.1016/j.jmb.2008.10.033.
80. Pelat T, Hust M, Hale M, Lefranc M-P, Dübel S, Thullier P. Isolation of a human-like antibody fragment (scFv) that neutralizes ricin biological activity. BMC Biotechnol (2009) 9:60. doi:10.1186/1472-6750-9-60.
81. Alamyar E, Giudicelli V, Duroux P, Lefranc M-P. Antibody V and C domain sequence, structure and interaction analysis with special reference to IMGT®. 2nd ed. In: Ossipow V, Fisher A, editors. Monoclonal Antibodies: Methods and Protocols. New York: Humana Press, Springer Science+Business Media (2014) (in press).
82. Lefranc M-P. How to use IMGT® for therapeutic antibody engineering. 2nd ed. In: Dübel S, Reichert J, editors. Handbook of Therapeutic Antibodies. Wiley (2014) (in press).
83. Wain HM, Bruford EA, Lovering RC, Lush MJ, Wright MW, Povey S. Guidelines for human gene nomenclature. Genomics (2002) 79:464-70. doi:10.1006/geno.2002.6748.
84. Bruford EA, Lush MJ, Wright MW, Sneddon TP, Povey S, Birney E. The HGNC database in 2008: a resource for the human genome. Nucleic Acids Res (2008) 36:D445-8. doi:10.1093/nar/gkm881.
85. Letovsky SI, Cottingham RW, Porter CJ, Li PW. GDB: the human genome database. Nucleic Acids Res (1998) 26(1):94-9. doi:10.1093/nar/26.1.94.
86. Maglott DR, Katz KS, Sicotte H, Pruitt KD. NCBI's LocusLink and RefSeq. Nucleic Acids Res (2000) 28(1):126-8. doi:10.1093/nar/28.1.126.
87. Maglott D, Ostell J, Pruitt KD, Tatusova T. Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res (2007) 35:D26-31. doi:10.1093/nar/gkl993.
88. Stabenau A, McVicker G, Melsopp C, Proctor G, Clamp M, Birney E. The Ensembl core software libraries. Genome Res (2004) 14:929-33. doi:10.1101/gr.1857204.
89. Wilming LG, Gilbert JG, Howe K, Trevanion S, Hubbard T, Harrow JL. The vertebrate genome annotation (Vega) database. Nucleic Acids Res (2008) 36:D753-60. doi:10.1093/nar/gkm987.
90. Kaas Q, Lefranc M-P. T cell receptor/peptide/MHC molecular characterization and standardized pMHC contact sites in IMGT/3Dstructure-DB. In silico Biol (2005) 5:505-28.
91. Kaas Q, Duprat E, Tourneur G, Lefranc M-P. IMGT standardization for molecular characterization of the T cell receptor/peptide/MHC complexes. In: Schoenbach C, Ranganathan S, Brusic V, editors. Immunoinformatics, New York: Springer (2008). p. 19-49.
92. Vlachakis D, Feidakis C, Megalooikonomou V, Kossida S. IMGT/Collier-de-Perles: a two-dimensional visualization tool for amino acid domain sequences. Theor Biol Med Model (2013) 10:14. doi:10.1186/1742-4682-10-14.
93. Lefranc M-P. Immunoinformatics of the V, C and G domains: IMGT® definitive system for IG, TR and IgSF, MH and MhSF. 2nd ed. In: De RK, Tomar N, editors. Immunoinformatics: From Biology to Informatics. Humana Press (2014) (in press).
94. Kabat EA, Wu TT, Perry HM, Gottesman KS, Foeller C. Sequences of Proteins of Immunological Interest. Washington, DC: U.S. Department of Health and Human Services (USDHHS), National Institute of Health NIH Publication (1991). p. 91-3242.
95. Chothia C, Lesk AM. Canonical structures for the hypervariable regions of immunoglobulins. Mol Biol (1987) 196(4):901-17. doi:10.1016/0022-2836(87)90412-8.
96. Frigoul A, Lefranc M-P. MICA: standardized IMGT allele nomenclature, polymorphisms and diseases. In: Pandalai SG, editor. Recent Research Developments in Human Genetics, Vol. 3. Trivandrum: Research Signpost (2005). p. 95-145.
97. Duprat E, Lefranc M-P, Gascuel O. A simple method to predict protein binding from aligned sequences-application to MHC superfamily and beta2-microglobulin. Bioinformatics (2006) 22:453-9. doi:10.1093/bioinformatics/bti826.
98. Hischenhuber B, Frommlet F, Schreiner W, Knapp B. MH2c: characterization of major histocompatibility α-helices-an information criterion approach. Comput Phys Commun (2012) 183(7):1481-90. doi:10.1016/j.cpc.2012.02.008.
99. Hischenhuber B, Havlicek H, Todoric J, Höllrigl-Binder S, Schreiner W, Knapp B. Differential geometric analysis of alterations in MH α-helices. J Comput Chem (2013) 34(21):1862-79. doi:10.1002/jcc.23328.
100. Rose PW, Beran B, Bi C, Bluhm WF, Dimitropoulos D, Goodsell DS, et al. The RCSB protein data bank: redesigned web site and web services. Nucleic Acids Res (2011) 39:D392-401. doi:10.1093/nar/gkq1021.
101. Riechmann L, Clark M, Waldmann H, Winter G. Reshaping human antibodies for therapy. Nature (1988) 332:323-7. doi:10.1038/332323a0.
102. Duprat E, Kaas Q, Garelle V, Lefranc G, Lefranc M-P. IMGT standardization for alleles and mutations of the V-LIKE-DOMAINs and C-LIKE-DOMAINs of the immunoglobulin superfamily. In: Pandalai SG, editor. Recent Research Developments in Human Genetics, Vol. 2. Trivandrum, Kerala: Research Signpost (2004). p. 111-36.
103. Bertrand G, Duprat E, Lefranc M-P, Marti J, Coste J. Characterization of human FCGR3B*02 (HNA-1b, NA2) cDNAs and IMGT standardized description of FCGR3B alleles. Tissue Antigens (2004) 64:119-31. doi:10.1111/j.1399-0039.2004.00259.x.
104. Bernard D, Hansen JD, du Pasquier L, Lefranc M-P, Benmansour A, Boudinot P. Costimulatory receptors in jawed vertebrates: conserved CD28, odd CTLA4 and multiple BTLAs. Dev Comp Immunol (2005) 31:255-71. doi:10.1016/j.dci.2006.06.003.
105. Garapati VP, Lefranc M-P. IMGT Colliers de Perles and IgSF domain standardization for T cell costimulatory activatory (CD28, ICOS) and inhibitory (CTLA4, PDCD1 and BTLA) receptors. Dev Comp Immunol (2007) 31:1050-72. doi:10.1016/j.dci.2007.01.008.
106. Hansen JD, Pasquier LD, Lefranc M-P, Lopez V, Benmansour A, Boudinot P. The B7 family of immunoregulatory receptors: a comparative and evolutionary perspective. Mol Immunol (2009) 46:457-72. doi:10.1016/j.molimm.2008.10.007.